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Fix MultiQC report generation #145

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merged 2 commits into from
Oct 17, 2023
Merged

Fix MultiQC report generation #145

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6018988
Remove multiqc channel reset
Aratz Oct 16, 2023
9236c6f
Update changelog
Aratz Oct 17, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

- [#127](https://github.com/nf-core/demultiplex/pull/127) Add `singularity.registry = 'quay.io'` and bump NF version to 23.04.0
- [#140](https://github.com/nf-core/demultiplex/pull/140) Make it possible to skip MultiQC, fix error raising
- [#145](https://github.com/nf-core/demultiplex/pull/145) Fix MultiQC report generation

## `Removed`

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8 changes: 4 additions & 4 deletions tests/pipeline/bclconvert.nf.test
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Expand Up @@ -20,10 +20,10 @@ nextflow_pipeline {
{ assert workflow.success },
{ assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") },
{ assert workflow.trace.succeeded().size() == 6 },
// FIXME https://github.com/nf-core/demultiplex/issues/64
// { assert snapshot(path("$outputDir/multiqc/multiqc_data/multiqc_bclconvert_bylane.txt"),
// path("$outputDir/multiqc/multiqc_data/multiqc_fastp.txt"),
// path("$outputDir/multiqc/multiqc_data/multiqc_bclconvert_bysample.txt")).match("multiqc") },
{ assert snapshot(path("$outputDir/multiqc/multiqc_data/multiqc_bclconvert_bylane.txt"),
path("$outputDir/multiqc/multiqc_data/multiqc_fastp.txt"),
path("$outputDir/multiqc/multiqc_data/multiqc_bclconvert_bysample.txt")
).match("multiqc") },
{ assert snapshot(path("$outputDir/220422_M11111_0222_000000000-K9H97/Sample1_S1_L001.fastp.fastq.gz"),
path("$outputDir/220422_M11111_0222_000000000-K9H97/Sample1_S1_L001_R1_001.fastq.gz"),
path("$outputDir/220422_M11111_0222_000000000-K9H97/Sample1_S1_L001_summary.txt"),
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1 change: 0 additions & 1 deletion workflows/demultiplex.nf
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Expand Up @@ -228,7 +228,6 @@ workflow DEMULTIPLEX {
methods_description = WorkflowDemultiplex.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description, params)
ch_methods_description = Channel.value(methods_description)

ch_multiqc_files = Channel.empty()
ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml'))
ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
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